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- PDB-3su0: Crystal structure of NS3/4A protease variant R155K in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3su0
TitleCrystal structure of NS3/4A protease variant R155K in complex with danoprevir
ComponentsGenome polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NS3 / drug resistance / drug design / Protease inhibitors / HCV / serine protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / host cell perinuclear region of cytoplasm / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / serine-type endopeptidase activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / : / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-TSV / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.159 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8844
Polymers20,9931
Non-polymers8913
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.279, 58.537, 60.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Genome polyprotein


Mass: 20992.844 Da / Num. of mol.: 1 / Mutation: L1039E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1a / Strain: BID-V318 / Gene: NS3-NS4A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical ChemComp-TSV / (2R,6S,12Z,13aS,14aR,16aS)-6-[(tert-butoxycarbonyl)amino]-14a-[(cyclopropylsulfonyl)carbamoyl]-5,16-dioxo-1,2,3,5,6,7,8 ,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-2-yl 4-fluoro-2H-isoindole-2-carboxylate / ITMN-191 / danoprevir


Mass: 729.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H44FN5O9S / Comment: inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.159→50 Å / Num. obs: 67429 / % possible obs: 97.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.055 / Χ2: 1.018 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.159-1.24.70.47161500.995190.4
1.2-1.255.80.40765881.007197.6
1.25-1.315.90.31366851.029198
1.31-1.3860.22967221.029198.4
1.38-1.4660.16567631.012198.6
1.46-1.576.10.11267571.002199.2
1.57-1.736.10.08168351.019199.4
1.73-1.9860.0768781.023199.8
1.98-2.560.05869701.0291100
2.5-505.80.03370811.025197.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M5M CHAIN B

3m5m


Resolution: 1.159→40.84 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.1624 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9084 / SU B: 0.96 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0342 / SU Rfree: 0.0335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 3391 5 %RANDOM
Rwork0.1527 ---
obs0.1537 67223 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.75 Å2 / Biso mean: 12.6627 Å2 / Biso min: 4.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.159→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 57 192 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221559
X-RAY DIFFRACTIONr_bond_other_d0.0010.021034
X-RAY DIFFRACTIONr_angle_refined_deg1.3232.0082145
X-RAY DIFFRACTIONr_angle_other_deg1.08332537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05622.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2091512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02308
X-RAY DIFFRACTIONr_mcbond_it1.1181.51002
X-RAY DIFFRACTIONr_mcbond_other0.3721.5415
X-RAY DIFFRACTIONr_mcangle_it1.80621617
X-RAY DIFFRACTIONr_scbond_it2.5153557
X-RAY DIFFRACTIONr_scangle_it3.634.5514
X-RAY DIFFRACTIONr_rigid_bond_restr0.94132593
LS refinement shellResolution: 1.159→1.189 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 244 -
Rwork0.223 4115 -
all-4359 -
obs--86.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6806-3.12262.007210.33097.372810.5360.2294-0.20090.1653-0.77490.0058-0.4727-0.6166-0.3139-0.23520.1478-0.02050.11930.0063-0.00330.00778.1606-20.602-1.9348
20.5121-0.3568-0.49721.97261.15642.11160.0078-0.02690.02310.02230.0343-0.0761-0.04640.0464-0.04220.01640.00040.00430.01320.00360.00773.3238-1.74620.3724
31.3731-0.5072-1.44571.41190.14222.47470.028-0.09330.0126-0.0571-0.0018-0.061-0.04940.093-0.02630.0257-0.0060.00810.01050.0010.00973.86485.351819.6832
42.0225-2.66570.39615.56022.50567.7540.0117-0.0906-0.0315-0.4860.1358-0.7137-0.42120.4442-0.14760.0479-0.01510.1170.00860.01890.137312.7706-5.729711.8583
515.76641.966-2.0612.20260.02754.97990.1016-0.36090.11310.1216-0.069-0.0737-0.09780.229-0.03270.0243-0.0137-0.00960.0091-0.0010.01266.0095-1.821326.6117
61.34370.96610.83981.62181.6875.73690.02320.11050.0494-0.08960.0376-0.04020.0089-0.0286-0.06080.03060.00980.00650.03060.01010.0124-0.0586-5.336813.0482
71.3049-0.64310.67340.5253-1.05713.48680.00110.00470.02330.00640.002-0.00590.0512-0.0199-0.00320.0259-0.001800.01220.00370.0132-1.6212-7.734823.0324
80.0313-0.106-0.15090.13620.20260.2416-0.01220.0094-0.02360.0172-0.01070.00080.0255-0.00840.02290.030.00520.00360.0211-0.00010.0275-2.6988-14.134519.0085
92.62151.57661.27371.83510.81161.62970.0345-0.0373-0.0681-0.0043-0.0313-0.14830.03740.057-0.00320.01010.00810.01440.02280.0030.034110.956-12.945816.2503
100.99650.35310.13840.27230.19830.468-0.0107-0.0108-0.01630.0296-0.0135-0.01090.02370.01040.02410.02370.00530.0030.01260.00230.0217-0.4288-17.89421.5853
118.9961.4526-6.82391.0531-0.6655.1594-0.0986-0.2784-0.13980.014-0.0219-0.05230.03730.18730.12050.02050.0125-0.01430.0469-0.00140.0074-0.9035-8.244434.5206
121.88851.308-2.22020.79-1.70584.6090.0041-0.03240.1817-0.01290.00980.10330.01580.0393-0.0140.01640.00780.01180.0073-0.00040.0513-11.22020.113226.8616
132.2060.8115-1.00270.3787-0.18060.84420.0895-0.00050.17650.0440.01650.04570.0314-0.085-0.10590.0141-0.00710.01550.03930.00370.032-18.302-4.142229.8656
140.5733-0.5002-0.20861.1685-0.44551.33720.03630.0045-0.032-0.03260.06020.1474-0.0372-0.1583-0.09660.01740.01250.01210.03650.02660.0377-21.6307-2.332225.0416
151.351-0.77782.46024.1295-1.00880.75240.0058-0.0683-0.00430.13490.0994-0.09620.0159-0.062-0.10520.01250.0190.00780.05150.03820.0204-15.47131.623515.5025
160.12790.0323-0.7837-0.0914-0.09883.73260.0228-0.01330.1048-0.01570.02250.055-0.0290.0892-0.04520.0218-0.00070.01590.0352-0.00920.0891-8.5626-4.537930.1663
171.7699-0.75471.49830.8965-0.63952.98970.0274-0.01110.0344-0.015-0.0654-0.02010.0698-0.04890.03790.0197-0.00390.00470.03310.00040.01-12.5428-9.124521.211
180.7911-0.0847-0.48883.3187-4.19796.5586-0.10460.1607-0.058500.25160.23980.0791-0.367-0.1470.0149-0.01930.00540.07110.02090.0338-22.575-3.351117.0994
193.8205-2.10822.25411.9167-2.26693.9744-0.0067-0.0304-0.04680.01120.07980.05740.0893-0.084-0.07310.0264-0.00120.00840.01470.00240.0091-12.455-13.139128.3253
2016.1308-0.758-5.60091.2569-1.0930.415-0.4827-0.4678-0.43960.0271-0.02090.03380.02280.07750.50360.0650.03690.01770.0020.04750.1307-5.2878-19.218430.5966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A983 - 988
2X-RAY DIFFRACTION2A989 - 1003
3X-RAY DIFFRACTION3A1004 - 1012
4X-RAY DIFFRACTION4A1013 - 1027
5X-RAY DIFFRACTION5A1028 - 1033
6X-RAY DIFFRACTION6A1034 - 1041
7X-RAY DIFFRACTION7A1042 - 1049
8X-RAY DIFFRACTION8A1050 - 1061
9X-RAY DIFFRACTION9A1062 - 1070
10X-RAY DIFFRACTION10A1071 - 1088
11X-RAY DIFFRACTION11A1089 - 1100
12X-RAY DIFFRACTION12A1101 - 1111
13X-RAY DIFFRACTION13A1112 - 1122
14X-RAY DIFFRACTION14A1123 - 1129
15X-RAY DIFFRACTION15A1130 - 1136
16X-RAY DIFFRACTION16A1137 - 1152
17X-RAY DIFFRACTION17A1153 - 1157
18X-RAY DIFFRACTION18A1158 - 1167
19X-RAY DIFFRACTION19A1168 - 1173
20X-RAY DIFFRACTION20A1174 - 1179

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